PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os10g28330.1
Common NameEhd2, LOC4348644, Os10g0419200, OSNPB_100419200, RID1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family C2H2
Protein Properties Length: 410aa    MW: 44267.4 Da    PI: 8.0487
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os10g28330.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.81.9e-053961123
                      EEETTTTEEESSHHHHHHHHHHT CS
           zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                      ++C+ C+k F r  nL+ H r H
  LOC_Os10g28330.1 39 FVCEVCNKGFQRDQNLQLHRRGH 61
                      89*******************88 PP

2zf-C2H213.30.00026124146123
                       EEETTTTEEESSHHHHHHHHHHT CS
           zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                       ++C+ Cgk++  +s+ k H +++
  LOC_Os10g28330.1 124 WRCERCGKRYAVHSDWKAHVKNC 146
                       58******************987 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.42E-73861No hitNo description
Gene3DG3DSA:3.30.160.608.3E-63861IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.973961IPR007087Zinc finger, C2H2
PfamPF121717.5E-53961IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.0213961IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002804161IPR007087Zinc finger, C2H2
SMARTSM003558989119IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.2E-4112144IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.42E-7119144No hitNo description
SMARTSM0035599124144IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009072anatomyplant ovary
PO:0007042developmental stagewhole plant fruit formation stage
Sequence ? help Back to Top
Protein Sequence    Length: 410 aa     Download sequence    Send to blast
MAAAQEPRAK KKRSLPGNPD PEAEVIALSP RALVATNRFV CEVCNKGFQR DQNLQLHRRG  60
HNLPWKLRHR AAAVSAVTTA APAPRKRVYV CPEPTCVHHD PARALGDLTG IKKHFSRKHG  120
EKRWRCERCG KRYAVHSDWK AHVKNCGTRE YRCDCGILFS RKDSLLTHRA FCDALAEESA  180
RLLAAANNSS SITTTTCNNS NISSNNNNNN INSISNSNNL LITSSSSSPP LFLPFSTTPA  240
ENPNPNQLLF LQQHQAAHHQ LLLPQFQQPP SSPPAYFDHL AFGGGGGVIT GSSCNDDNSS  300
IAGDVMVAAG GDSVSFGLTS EGSVTMHAGD VGRRRLTRDF LGVDHDAGEV DELELDELPA  360
DLSTTAAACQ GCNFAAATTA ACCATDFTTG SRQYLGRLPP VNETWSHNF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C6e-33120188371Zinc finger protein JACKDAW
5b3h_F6e-33120188371Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.632820.0flower| panicle
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2000963920.0
Expression AtlasB1B534-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Detected in young expanded leaves emerging from the culms (PubMed:18774969). In young panicles, accumulates in spikelets and panicle branches (PubMed:18774969). Under short days (SD), observed in leaves by 1 week after germination and reaches a peak by 2 weeks. Subsequently, the level gradually decreases, but maintains at low levels even after flowering (about 9 weeks) (PubMed:18790997). Under long days (LD), present in leaves at low levels during all developmental stages from at least 1 week after germination (PubMed:18790997). {ECO:0000269|PubMed:18774969, ECO:0000269|PubMed:18790997}.
UniprotTISSUE SPECIFICITY: Mostly expressed in developing leaves (more in sheaths than in blades, especially in the outer epidermal cell of immature leaves and in the region immediately beneath the meristem where internodes are visible) and panicles, and, at very low levels, around the shoot apex and in roots. {ECO:0000269|PubMed:18725639, ECO:0000269|PubMed:18774969, ECO:0000269|PubMed:18790997, ECO:0000269|PubMed:24280027}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that acts as a flowering master switch in both long and short days, independently of the circadian clock (PubMed:18790997, PubMed:18725639, PubMed:18774969, PubMed:19304997, PubMed:24280027). Promotes flowering upstream of HD1 by up-regulating FTL1, FTL4, FTL5, FTL6, EHD1, HD3A and RFT1 (PubMed:18790997, PubMed:18725639, PubMed:18774969). Seems to repress FTL11 expression (PubMed:18725639). May recognize the consensus motif 5'-TTTGTCGTAAT-3' in target gene promoters (PubMed:18725639). {ECO:0000269|PubMed:18725639, ECO:0000269|PubMed:18774969, ECO:0000269|PubMed:18790997, ECO:0000269|PubMed:24280027, ECO:0000303|PubMed:19304997}.
Function -- GeneRIF ? help Back to Top
  1. Suppressor of rid1 (SID1) encodes an INDETERMINATE DOMAIN (IDD) transcription factor, and both SID1 and Rice Indeterminate 1 (RID1) directly target the promoter regions of florigen genes.
    [PMID: 28234896]
  2. These results demonstrate that OsCOL15 is an important floral regulator acting upstream of Ghd7 and RID1 in the rice photoperiodic flowering-time regulatory network.
    [PMID: 29154991]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00673SELEXTransfer from GRMZM2G011357Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os10g28330.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by FKF1 (PubMed:25850808). Down-regulated by DLF1 (PubMed:25036785). During the basic vegetative growth phase (BVP, photoperiod-insensitive phase), suppressed via phytochrome-mediated light signals involving the phytochromobilin synthase HY2 (PubMed:25573482). {ECO:0000269|PubMed:25036785, ECO:0000269|PubMed:25573482, ECO:0000269|PubMed:25850808}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs10g28330
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB3591960.0AB359196.1 Oryza sativa Japonica Group Ehd2 mRNA for early heading date 2, complete cds, cultivar: Tohoku IL9.
GenBankFJ0095780.0FJ009578.1 Oryza sativa Japonica Group cultivar Zhonghua 11 Cys2/His2-type zinc finger transcription factor (RID1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015614407.10.0protein indeterminate-domain 12
SwissprotB1B5340.0EHD2_ORYSJ; Protein EARLY HEADING DATE 2
TrEMBLA0A0E0QZ670.0A0A0E0QZ67_ORYRU; Uncharacterized protein
STRINGORUFI10G10700.10.0(Oryza rufipogon)
STRINGOS10T0419200-000.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP130962832
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.13e-91C2H2 family protein
Publications ? help Back to Top
  1. Rice Chromosome 10 Sequencing Consortium
    In-depth view of structure, activity, and evolution of rice chromosome 10.
    Science, 2003. 300(5625): p. 1566-9
    [PMID:12791992]
  2. Wu C, et al.
    RID1, encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice.
    Proc. Natl. Acad. Sci. U.S.A., 2008. 105(35): p. 12915-20
    [PMID:18725639]
  3. Park SJ, et al.
    Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod.
    Plant J., 2008. 56(6): p. 1018-29
    [PMID:18774969]
  4. Song Y,Gao Z,Luan W
    Interaction between temperature and photoperiod in regulation of flowering time in rice.
    Sci China Life Sci, 2012. 55(3): p. 241-9
    [PMID:22527521]
  5. Hu S, et al.
    A point mutation in the zinc finger motif of RID1/EHD2/OsID1 protein leads to outstanding yield-related traits in japonica rice variety Wuyunjing 7.
    Rice (N Y), 2013. 6(1): p. 24
    [PMID:24280027]
  6. Cai Y, et al.
    Dlf1, a WRKY transcription factor, is involved in the control of flowering time and plant height in rice.
    PLoS ONE, 2014. 9(7): p. e102529
    [PMID:25036785]
  7. Yoshitake Y, et al.
    The effects of phytochrome-mediated light signals on the developmental acquisition of photoperiod sensitivity in rice.
    Sci Rep, 2015. 5: p. 7709
    [PMID:25573482]
  8. Han SH,Yoo SC,Lee BD,An G,Paek NC
    Rice FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1) promotes flowering independent of photoperiod.
    Plant Cell Environ., 2015. 38(12): p. 2527-40
    [PMID:25850808]
  9. Jin J, et al.
    MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice.
    Plant Physiol., 2015. 168(4): p. 1275-85
    [PMID:25855537]
  10. Deng L, et al.
    Suppressor of rid1 (SID1) shares common targets with RID1 on florigen genes to initiate floral transition in rice.
    PLoS Genet., 2017. 13(2): p. e1006642
    [PMID:28234896]
  11. Brambilla V,Gomez-Ariza J,Cerise M,Fornara F
    The Importance of Being on Time: Regulatory Networks Controlling Photoperiodic Flowering in Cereals.
    Front Plant Sci, 2017. 8: p. 665
    [PMID:28491078]
  12. Wu W, et al.
    The rice CONSTANS-like protein OsCOL15 suppresses flowering by promoting Ghd7 and repressing RID1.
    Biochem. Biophys. Res. Commun., 2018. 495(1): p. 1349-1355
    [PMID:29154991]